Gibbons-Lab/ccmb_workshop

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Gibbons-Lab/ccmb_workshop

Gibbons-Lab

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Data and materials for the CCMB workshop on Cloud Computing and Microbiome Bioinformatics.

isb_course_2020

Materials and tutorials for the 2020 ISB Microbiome Course

Jupyter Notebook

isb_course_2023

Materials and presentation for the 2023 ISB Microbiome course.

Jupyter Notebook

isb_course_2022

Materials and presentation for the 2022 ISB Microbiome course.

Jupyter Notebook

isb_course_2021

Materials and presentations for the 2021 ISB Virtual Microbiome Series.

Jupyter Notebook

mbtools

R package for microbiome analysis. Provides helper functions for common workflows ranging from preprocessing to visualization.

pipelines

Pipelines used in the lab.

human-microbiome-time-series-growth-phase-estimation

Analysis script for article "Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes."

2021_microbiome_course_utils

A small Python package used for the course.

2021_gene_environment_interactions

Notebooks, code and intermediate data for the Arivale gene-environment interactions.

Jupyter Notebook

manuals-and-policies

weight_loss_2019

Data and scripts for the weight loss project funded by the Innovator Award.

aquaponics

Analysis code and scripts for the Aquaponics collab with Jessica Day et. al.

evan_rotation_notebooks

Repository for Evan Pepper's Fall 2020 Rotation

Jupyter Notebook

cdiff_invasion

Jupyter Notebook

2021_data_literacy

Data for the Data Literacy initiative

american_gut

Project materials to analyze the American Gut data set.

Jupyter Notebook

wiki

General good-to-know stuff.

Generally-Healthy-Cohort-BMF

Generally-healthy individuals with aberrant bowel movement frequencies show enrichment for microbially-derived blood metabolites associated with impaired kidney function.

american-gut-app

Source repository for the American Gut App.

mmmih

Materials and slides for the 3rd Microbiome Movement – Maternal & Infant Health Summit 2021.